[English] 日本語
Yorodumi
- PDB-1mlm: STRUCTURAL AND FUNCTIONAL EFFECTS OF APOLAR MUTATIONS OF VAL68(E1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mlm
TitleSTRUCTURAL AND FUNCTIONAL EFFECTS OF APOLAR MUTATIONS OF VAL68(E11) IN MYOGLOBIN
ComponentsMYOGLOBIN
KeywordsOXYGEN STORAGE
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Globin / Myoglobin / Globin-like superfamily / Globin/Protoglobin / Globin / Globins / Globin-like / Orthogonal Bundle / Mainly Alpha
Myoglobin
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsQuillin, M.L. / Phillips Jr., G.N.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Structural and functional effects of apolar mutations of the distal valine in myoglobin.
Authors: Quillin, M.L. / Li, T. / Olson, J.S. / Phillips Jr., G.N. / Duo, Y. / Ikeda-Saito, M. / Regan, R. / Carlson, M. / Gibson, Q.H. / Li, H. / Elber, R.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: High-Resolution Crystal Structures of Distal Histidine Mutants of Sperm Whale Myoglobin
Authors: Quillin, M.L. / Arduini, R.M. / Olson, J.S. / Phillips Jr., G.N.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: A Novel Site-Directed Mutant of Myoglobin with an Unusually High O2 Affinity and Low Autooxidation Rate
Authors: Carver, T.E. / Brantley Junior, R.E. / Singleton, E.W. / Arduini, R.M. / Quillin, M.L. / Phillips Jr., G.N. / Olson, J.S.
#3: Journal: Proteins / Year: 1990
Title: Crystal Structure of Myoglobin from a Synthetic Gene
Authors: Phillips Jr., G.N. / Arduini, R.M. / Springer, B.A. / Sligar, S.G.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 15, 1994-
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1204
Polymers17,3791
Non-polymers7413
Water2,720151
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)91.200, 91.200, 45.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Atom site foot note1: RESIDUE ILE 68 HAS BEEN MODELED IN TWO CONFORMATIONS. / 2: THIS CARBON IS COORDINATED WITH FE OF THE HEME GROUP.

-
Components

#1: Protein/peptide MYOGLOBIN /


Mass: 17379.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / References: UniProt: P02185
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Sulfate
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Heme
#4: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO / Carbon monoxide
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O / Water

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal grow
*PLUS
pH: 9 / Method: batch method / Details: micro seeding
Components of the solutions
*PLUS

Crystal-ID: 1 / Sol-ID: 1

IDConc.Common name
160 mg/mlprotein
22.4 Mammonium sulfate
315 mMTris-HCl
40.75 mMEDTA

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / % possible obs: 88.7 % / Rmerge(I) obs: 0.102

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.1611 / Rfactor obs: 0.1611 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 0 50 151 1427
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.265
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.88
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d4.502
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.1611
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d2.265
X-RAY DIFFRACTIONx_dihedral_angle_d21.889

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more